Merge branch 'development' into plasma_chamber_ultimate

Author: ajnonaka

Docs/Makefile

@@ -28,6 +28,3 @@ Python-build:
 
 Doxygen-build:
 	doxygen Doxyfile
-
-Latex-conversion:
-	cd source/latex_theory; make

Docs/README.md

@@ -27,12 +27,3 @@ In order to remove all of the generated files, use:
 ```
 make clean
 ```
-
-### Regenerating the theory documentation
-
-The theory is generated from Latex sources in PICSAR, and the resulting `.rst`
-files are stored in the current repo, in `source/latex_theory`. In order to
-regenerate the theory documentation:
-```
-make Latex-conversion
-```

Docs/requirements.txt

@@ -11,7 +11,7 @@ docutils>=0.17.1
 
 # PICMI API docs
 # note: keep in sync with version in ../requirements.txt
-picmistandard==0.33.0
+picmistandard==0.34.0
 # for development against an unreleased PICMI version, use:
 # picmistandard @ git+https://github.com/picmi-standard/picmi.git#subdirectory=PICMI_Python
 

Docs/source/conf.py

@@ -81,7 +81,7 @@ def download_with_headers(url, filename):
 templates_path = ["_templates"]
 
 # Relative path to bibliography file, bibliography style
-bibtex_bibfiles = ["latex_theory/allbibs.bib", "refs.bib"]
+bibtex_bibfiles = ["refs.bib"]
 
 
 # An brief introduction to custom BibTex formatting can be found in the Sphinx documentation:

Docs/source/dataanalysis/picviewer.rst

@@ -2,7 +2,7 @@ PICViewer
 =========
 
 .. figure:: sample_image.png
-   :alt: picture
+   :alt: Figure not found
 
 PICViewer is a visualization GUI implemented on PyQt.
 The toolkit provides various easy-to-use functions for data analysis of

Docs/source/dataanalysis/visit.rst

@@ -26,7 +26,7 @@ Assuming that you ran a 2D simulation, here are instructions for making a simple
 Your image should look similar to the one below
 
 .. figure:: Ez.png
-   :alt: picture
+   :alt: Figure not found
 
 
 In 3D, you must apply the “Operators” -> “Slicing”

Docs/source/dataanalysis/visualpic.rst

@@ -32,9 +32,11 @@ Example: ``vpic3d -s beam -rho -Ez diags/diag1/`` could be used to visualize the
 Example: ``vpic3d -Ex diags/diag1/`` could be used to visualize the transverse focusing field :math:`E_x` in a plasma wake behind a laser pulse (linearly polarized in :math:`E_y`), see below:
 
 .. figure:: https://user-images.githubusercontent.com/1353258/233236692-4d75b12f-de44-43dc-97bd-c96b04ee68ac.png
-   :alt: Example view of a 3D rendering with VisualPIC.
+   :alt: Figure not found
    :width: 100%
 
+   Example view of a 3D rendering with VisualPIC.
+
 The **Python script** controlled rendering allows more flexible options, such as selecting and cutting views, rendering directly into an image file, looping for animations, etc.
 As with matplotlib scripts, Python script scenes can also be used to open a GUI and then browse time series interactively.
 The `VisualPIC examples <https://github.com/AngelFP/VisualPIC/tree/dev/examples>`__ provide showcases for scripting.

Docs/source/dataanalysis/workflows/tunneling.rst

@@ -52,5 +52,7 @@ To close the connection down, do this:
   * ``Ctrl+C`` the SSH tunnel in terminal B
 
 .. figure:: https://user-images.githubusercontent.com/1353258/232120440-3965fa38-9ca6-4621-a100-2da74eb899cf.png
-   :alt: Example view of remote started Jupyter service, active SSH tunnel, and local browser connecting to the service.
+   :alt: Figure not found
    :width: 100%
+
+   Example view of remote started Jupyter service, active SSH tunnel, and local browser connecting to the service.

Docs/source/developers/checksum.rst

@@ -27,13 +27,11 @@ In addition, WarpX is a *highly-parallel and highly-optimized code*:
 Contact us
 ^^^^^^^^^^
 
-If you are starting using WarpX, or if you have a user question, please pop in our `discussions page <https://github.com/BLAST-WarpX/warpx/discussions>`__ and get in touch with the community.
+The `WarpX GitHub repository <https://github.com/BLAST-WarpX/warpx>`__ is the main communication platform:
 
-The `WarpX GitHub repo <https://github.com/BLAST-WarpX/warpx>`__ is the main communication platform.
-Have a look at the action icons on the top right of the web page: feel free to watch the repo if you want to receive updates, or to star the repo to support the project.
-For bug reports or to request new features, you can also open a new `issue <https://github.com/BLAST-WarpX/warpx/issues>`__.
-
-We also have a `discussion page <https://github.com/BLAST-WarpX/warpx/discussions>`__ on which you can find already answered questions, add new questions, get help with installation procedures, discuss ideas or share comments.
+   - If you are new to WarpX or have a question, we encourage you to visit our `discussions page <https://github.com/BLAST-WarpX/warpx/discussions>`__ and connect with the community. This page is also a great place to browse answers to previously asked questions, post new ones, get help with installation, exchange ideas, and share feedback.
+   - You can also explore the icons in the upper right corner of the `WarpX GitHub repository <https://github.com/BLAST-WarpX/warpx>`__ (e.g., ``Watch``, ``Star``, etc.): feel free to watch the repository if you want to receive updates, or to star the repository to support the project.
+   - For bug reports, feature requests, or installation issues, you can also open a new `issue <https://github.com/BLAST-WarpX/warpx/issues>`__.
 
 .. raw:: html
 
@@ -120,15 +118,9 @@ Theory
    :caption: THEORY
    :maxdepth: 1
    :hidden:
+   :titlesonly:
 
    theory/intro
-   theory/pic
-   theory/amr
-   theory/boundary_conditions
-   theory/boosted_frame
-   theory/multiphysics_extensions
-   theory/kinetic_fluid_hybrid_model
-   theory/cold_fluid_model
 
 Development
 -----------